The best way I have found to have an option similar to  the Make Payment that used to be on the right side of the list of bills is to open the Vendor Transaction List for the vendor you wish to pay, go to "New Transaction" in the upper right, drop down to select "Check". This will open the Check window and you should find the list of bills to be paid to that vendor on the right. You can then click on the ones you wish to pay with that check. You do have to click on each bill rather than having the old option of checking the box at the top of the list of bills to mark them all as being paid on one check. Repeat the process depending on how many invoices you wish to pay per check. The bills will then be marked as "PAID" in your vendor ledger. I was also very frustrated, but I do hope that this helps.